Bacterial Community Function Research Articles

Enhancing the engineering design of diversion routes to safeguard water quality: New insights from a carbon cycling perspective

<p>Conserving the quality of transferred water ensures the success and sustainability of interbasin water diversion works, which are increasingly crucial for global water security. Despite intensive scientific and engineering efforts, carbon dynamics in these artificial rivers have been overlooked. The accumulation of organic mud in some water transfer canals, for example, in the Middle Route of the South-to-North Water Diversion (SNWT) in China, poses multifaceted risks, including jeopardized water quality, disrupted water supply, and surging mud removal expenses. In contrast, natural channels for water delivery, such as the parallel East Route of the SNWT, do not experience mud accumulation challenges. Our study reveals that the open concrete canal of the Middle Route, devoid of connections to local water bodies, compromises hydrological connectivity, contrasting with the East Route, which enhances it. This, in turn, undermines microbial stochastic assembly processes, impedes the introduction of habitat-generalist microbial species, and facilitates detrital carbon accumulation within the ecosystem, presumably due to constraints on bacterial community functions. These findings can improve future engineering designs of water transfer schemes, including water diversion approaches and channel construction, for preserving transferred water quality.</p>

Current state, microbiological monitoring, and prevention of water pollution in Lake Baikal

Since 2003, Limnological Institute SB RAS has been holding the International Baikal Microbiological Symposia “Microorganisms and Viruses in Aquatic Ecosystems” every four years, and even in the “covid” year 2020, it was held “in remote mode.” The proper functioning of viral and bacterial communities is the basis for the stable quality of aquatic ecosystems. New ecological problems for the Lake Baikal ecosystem are becoming more and more acute, and the scientific research, the results of which are presented and discussed at these symposia for different aquatic ecosystems around the world, should help to find solutions for preserving the water quality now and in the future. We analyze the long-term microbiological studies of the water quality in the littoral and pelagic zones of Lake Baikal carried out by numerous authors, and propose a specific scheme of microbiological monitoring of this unique aquatic ecosystem required by the environmental regulatory authorities. Specific measures to prevent pollution of oligotrophic lake waters are also provided; these measures can be rapidly implemented now.

Characteristics of bacterial community and extracellular enzymes in response to atrazine application in black soil

The ecological functioning of black soil largely depends on the activities of various groups of microorganisms. However, little is known about how atrazine, a widely used herbicide with known harmful effects on the environment, influences the microbial ecology of black soil, and the extracellular enzymes related to the carbon, nitrogen and phosphorus cycles. Here, we evaluated the change in extracellular enzymes and bacterial community characteristics in black soil after exposure to various concentrations of atrazine. Low concentrations of applied atrazine (10 – 20 mg kg−1) were almost completely degraded after 120 days. At high concentrations (80 – 100 mg kg−1), about 95% of the applied atrazine was degraded over the same period. Additionally, linear fitting of data indicated that the total enzymatic activity index (TEI) and bacterial α-diversity index were negatively correlated with atrazine applied concentration. The atrazine had a greater effect on bacterial beta diversity after 120 days, which differentiated species clusters treated with low and high atrazine concentrations. Soil bacterial community structure and function were affected by atrazine, especially at high atrazine concentrations (80 – 100 mg kg−1). Key microorganisms such as Sphingomonas and Nocardioides were identified as biomarkers for atrazine dissipation. Functional prediction indicated that most metabolic pathways might be involved in atrazine dissipation. Overall, the findings enhance our understanding of the factors driving atrazine degradation in black soil and supports the use of biomarkers as indicators of atrazine dissipation.

Independent and combined effects of microplastics pollution and drought on soil bacterial community

Global terrestrial ecosystems are simultaneously threatened by multiple environmental pressures, with microplastics (MPs) pollution and drought possibly being the most pressing, both of which may have unanticipated effects on soil organisms. Here, we investigated the responses of diversity, composition and functions of soil bacterial community to MPs pollution (including two MPs types: polyethylene (PE) and polylactic acid (PLA); two MPs sizes: < 20 μm and <300 μm) and drought in microcosms. We found that only 20 μm PLA MPs significantly decreased soil bacterial diversity by 17.4 % and altered soil bacterial community composition, while PE MPs and 300 μm PLA MPs had no significant effects. The copiotrophic bacteria (i.e., Proteobacteria and Firmicutes) were enriched in the 20 μm PLA MPs pollution soils due to the enhanced dissolved organic carbon contents. Moreover, our results showed that the 20 μm PLA MPs also affected the potential phenotypes and functions of soil bacterial community, increasing the potentially pathogenic, stress-tolerant, containing mobile elements and forming biofilms phenotypes, and promoting membrane transport and signal transduction pathways. These results suggested that the effects of MPs on soil bacterial community varied depending on MPs types and sizes. However, drought significantly increased soil bacterial diversity by 10.3 % and affected soil bacterial community composition in the 20 μm PLA MPs pollution soils. We also found that drought inhibited the levels of potentially pathogenic, containing mobile elements and forming biofilms phenotypes in the 20 μm PLA MPs pollution soils. Taken together, these findings reveal that drought may alleviate the adverse effects of MPs pollution on soil bacterial community, which enhances our understanding of the interactive effects of multiple global change factors on agroecosystem functions.

Soil nutrients drive changes in the structure and functions of soil bacterial communities in a restored forest soil chronosequence

The restoration of plants is effective for restoring ecosystems in eroded areas. Soil bacterial communities play an important role in nutrient cycling. High-throughput sequencing technology was used to determine the changes in soil bacteria in different restored plant communities and years of restoration. The FAPROTAX database and random forest model were also used to analyze the changes in soil bacterial carbon (C), nitrogen (N), and phosphorus (P) metabolic functions and their influencing factors. The results showed that the bacterial community diversity, soil texture, physicochemical properties, and multifunctionality improved substantially with the increments and years of restoration. These changes, in turn, altered the nutrient metabolic functions in soils by increasing the fixation of bacterial C, decreasing the fixation of N, and gradually relieving the limitations on N. However, these changes also increased the limitation of P during the late stage of restoration. The pH values and soil nutrients were crucial and exerted a large influence on the nutrients and metabolic functions of the bacteria. These findings facilitate the restoration of plants in subtropical areas of eroded soil.

Heavy metal contamination impacts the structure and co-occurrence patterns of bacterial communities in agricultural soils.

Heavy metal (HM) contamination caused by mining and smelting activities can be harmful to soil microbiota, which are highly sensitive to HM stress. Here, we explore the effects of HM contamination on the taxonomic composition, predicted function, and co-occurrence patterns of soil bacterial communities in two agricultural fields with contrasting levels of soil HMs (i.e., contaminated and uncontaminated natural areas). Our results indicate that HM contamination does not significantly influence soil bacterial α diversity but changes the bacterial community composition by enriching the phyla Gemmatimonadetes, Planctomycetes, and Parcubacteria and reducing the relative abundance of Actinobacteria. Our results further demonstrate that HM contamination can strengthen the complexity and modularity of the bacterial co-occurrence network but weaken positive interactions between keystone taxa, leading to the gradual disappearance of some taxa that originally played an important role in healthy soil, thereby possibly reducing the resistance of bacterial communities to HM toxicity. The predicted functions of bacterial communities are related to membrane transport, amino acid metabolism, energy metabolism, and carbohydrate metabolism. Among these, functions related to HM detoxification and antioxidation are enriched in uncontaminated soils, while HM contamination enriches functions related to metal resistance. This study demonstrated that microorganisms adapt to the stress of HM pollution by adjusting their composition and enhancing their network complexity and potential ecological functions.

Grazing-driven shifts in soil bacterial community structure and function in a typical steppe are mediated by additional N inputs

Herbivore grazing and nitrogen (N) fertilization affect soil microbial diversity and community composition both in direct and indirect pathways (e.g., via alterations in soil microenvironment and plant communities); however, their combination effects are still largely unexplored. We carried out a field study to investigate how soil abiotic properties, plant community composition and functional traits altered soil bacterial community structure and function in response to a long-term herbivore grazing (17-year sheep grazing with four stocking rates) and anthropogenic N inputs (6-year N addition with four levels) experiment. We show that a high stocking rate of 8.7 sheep ha−1 (SR8.7) decreased soil bacterial α- and β-diversity, while α- and β-diversity showed hump-shaped and saddle-shaped responses, respectively, with increasing N addition rate, reaching tipping points at the N application rate of 10 g N m−2 year−1 (N10). The synergistic effects of grazing and N addition induced the highest soil bacterial α-diversity at SR2.7 with N10. The contrasting effects of grazing and N addition induced higher soil bacterial β-diversity at SR8.7 with N20. Plant factors (e.g., aboveground biomass of Stipa bungeana and community-weighted mean carbon [CWM_C]), edaphic factors (e.g., soil moisture, pH, NO3−-N, and C:nutrients ratios) and their interactions were the most significant factors affecting the diversity and community composition of bacteria. Our structure equation model (SEM) shows that grazing-induced negative effects on soil pH and plant community composition indirectly increased the β-diversity of soil bacteria, while grazing-induced decreased CWM_C had positive effects on bacterial α-diversity and community structure. However, N addition indirectly increased β-diversity of soil bacteria via changes in soil NO3−-N and plant community composition, while N addition had negative impacts on bacterial α-diversity and community structure via variations in CWM_C. The interaction of grazing and N addition increased the complexity and stability of the bacterial network. Based on the KEGG database, grazing and N addition could accelerate the soil functional potential of C and N cycling. Our findings suggest that N application at a rate of <10 g N m−2 year−1 with a stocking rate of <5.3 sheep ha−1 could maintain the development of soil bacteria in supporting the most important ecosystem functions and services. Complex responses of soil microbes to grazing and N addition indicate the need for deeper investigations of the impacts of global change on microbial involvement in biogeochemical cycles.

The Long-Term Application of Controlled-Release Nitrogen Fertilizer Maintains a More Stable Bacterial Community and Nitrogen Cycling Functions Than Common Urea in Fluvo-Aquic Soil

Controlled-release nitrogen fertilizer (CRNF) has been proven to surpass common urea by mitigating nutrient losses, enhancing soil quality, and improving crop productivity. However, the long-term effects of CRNF on soil biological properties are not well understood. Here, a 12-year field experiment was conducted with five treatments: no N fertilizer (PK); the split application of urea at the farmer’s practice rate (FP) and the optimal rate (OPT); the one-time application of CRNF at the same rate as the OPT (CRNF); and a 20% reduced rate of the OPT (0.8CRNF). Soil samples were collected during the maize tasseling and filling stages; high-throughput sequencing and the PICRUSt2 method were employed to determine the bacterial community and its functional potential. The results showed that CRNF significantly increased alkaline hydrolysis N by 14.10% and 9.45% compared to OPT during the tasseling and filling stages, respectively. This increase in soil available N resulted in a significant increase in bacterial diversity of 2.09% and 2.35% compared with the FP and OPT, respectively. The bacterial community in the FP and OPT changed markedly between the tasseling and filling stages, with many bacterial species at the ASV and genus levels showing variations in relative abundance. In contrast, CRNF and 0.8CRNF exhibited stable N-cycling functions, as indicated by the lower variations in nitrate reductase and predicted N-cycling functional genes between the tasseling and filling stages. The obtained results suggest that CRNF application can enhance soil N supply, promote the formation of stable bacterial communities, and maintain stable N-cycling functions.

Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat.

Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.

Filtration effect of Cordyceps chanhua mycoderm on bacteria and its transport function on nitrogen.

During the natural growth of Cordyceps chanhua, it will form a mycoderm structure specialized from hyphae. We found that the bacterial membrane of C. chanhua not only filters environmental bacteria but also absorbs and transports nitrogen elements inside and outside the body of C. chanhua. These findings are of great significance for understanding the stable mechanism of the internal microbial community maintained by C. chanhua and how C. chanhua maintains its own nutritional balance. In addition, this study also enriched our understanding of the differences in bacterial community composition and related bacterial community functions of C. chanhua at different growth stages, which is of great value for understanding the environmental adaptation mechanism, the element distribution network, and the changing process of symbiotic microbial system after Cordyceps fungi infected the host. At the same time, it can also provide a theoretical basis for some important ecological imitation cultivation technology of Cordyceps fungi.

Application of rhizobacteria to improve microbial community structure and maize (Zea mays L.) growth in saline soil.

The utilization of plant growth-promoting rhizobacteria (PGPR) has emerged as a prominent focus in contemporary research on soil microbiology, microecology, and plant stress tolerance. However, how PGPR influence the soil bacterial community and related ecological functions remains unclear. The aim of this study was to investigate the effects of three natural PGPR inoculations (YL07, Planococcus soli WZYH02; YL10, Bacillus atrophaeus WZYH01; YL0710, Planococcus soli WZYH02 and Bacillus atrophaeus WZYH01) on maize (Zea mays L.) growth under two salt stress conditions (S1, ECe = 2.1 ~ 2.5 dS/m; S2, ECe = 5.5 ~ 5.9 dS/m). The results revealed that compared to the control (CK), the average plant height of maize seedlings significantly increased by 27%, 23%, and 29% with YL07, YL10, and YL0710 inoculation under S1 conditions, respectively, and increased by 30%, 20%, and 18% under S2 conditions, respectively. Moreover, PGPR inoculation positively influenced the content of superoxide dismutase, catalase, soluble sugar, and proline in maize under salt stress. Subsequent analysis of alpha diversity indices, relative microbial abundance, principal coordinate analysis, cladograms, and linear discriminant analysis effect size histograms indicated significant alterations in the rhizosphere microbial community due to PGPR inoculation. FAPROTAX analysis demonstrated that YL10 inoculation in S2 rhizosphere soil had a notable impact on carbon cycle functions, specifically chemoheterotrophy, fermentation, and phototrophy. Thus, this study provides evidence that PGPR inoculation improves soil microbial communities and plant indices under salt stress. These findings shed light on the potential of PGPR as a viable approach for enhancing plant stress tolerance and fostering sustainable agricultural practices.

Comparison of soil microbial abundances and co-occurrence networks in the volcanic soil of the cone and crater

Volcanism changes the earth's surface building environments where new ecosystems can be constructed. However, the effects of volcanic environmental conditions (e.g. soil moisture, soil organic matter, and available K) on soil microbial communities remains unclear. In the present study, soil samples were collected from two natural habitats (the cone and crater) in Nushan Volcano, China, to investigate the abundances (absolute and relative), compositions, and functions of soil bacterial and fungal communities. The results showed higher 16S rRNA copies, and ITS rRNA copies in the crater compared to the cone. The bacterial and fungal diversities in the crater were higher than in the cone. The soil of the cone and crater displayed distinct bacterial and fungal community compositions based on the nonmetric multidimensional scaling (NMDS). Co-occurrence network analysis revealed the interspecific relationship of soil bacterial and fungal communities was closer in the cone with more links. The number of keystone taxa in the cone was higher than that in the crater. Meanwhile, Nordella and Arthrobacter in bacteria and Stilbella, Tausonia, and Marasmius in fungi were found as the keystone taxa. Moreover, structural equation models (SEM) revealed that soil physicochemical properties had the greatest impact on the composition of bacteria and fungi. Overall, the results advance further research on the effects of microbes on the functions and services of associated ecosystems in extreme environments.

Underestimated indirect and persistent effects of decaying macrophytes on aquatic ecosystem through alteration of bacterial community structure and function

The rapid release of nutrients by aquatic macrophyte decomposition directly results in the degradation of water quality and the deterioration of aquatic ecosystems. However, decaying macrophytes have indirect negative effects, mediated by bacteria in aquatic ecosystems, which may have long been underestimated. In this study, 16S rRNA sequencing was used to investigate the structural succession, possible metabolic function shifts, and specific environmental drivers of the bacterial community during the decomposition of four typical aquatic macrophytes over 188 days. Results indicate that nutrients released by macrophyte residues alter the physiochemical properties of overlaying water and have dual concentration effects of low promotion and high inhibition on α- and β-diversity of bacteria, driving their succession in different directions. High nutrient concentrations not only resulted in more substantial changes in the abundance of dominant bacteria at various taxonomic levels, but also inhibited carbon and nitrogen metabolic functions while promoting the phosphorus and sulfur metabolic functions of the bacterial community, which was in contrast to the effects of low nutrient concentrations. These effects persisted for a long time, potentially leading to a decrease in redundant genes and the loss of rare functional genes. This, in turn, indirectly reducing the structural stability of aquatic ecosystems and their resilience to external disturbances. Our findings indicate that the indirect and persistent negative impacts of macrophyte decomposition on aquatic ecosystems should not be ignored and that macrophyte residues should be harvested and properly treated before they undergoing explosive nutrient release.

Responses of greenhouse gas emissions to aeration coupled with functional membrane during industrial-scale composting of dairy manure: Insights into bacterial community composition and function

Greenhouse gas (GHG) emissions from manure management processes deserve more attention. Using three industrial-scale experiments, this study comprehensively evaluated the effects of different aeration coupled with semi-permeable membrane-covered strategies on the structure and function of bacterial communities and their impact on GHG emissions during dairy manure aerobic composting. The succession of the bacterial communities tended to be consistent for similar aeration strategies. Ruminiclostridium and norank_f__MBA03 were significantly positively correlated with the methane emission rate, and forced aeration coupled with semi-permeable membrane-covered decreased GHG emissions by inhibiting these taxa. Metabolism was the most active function of the bacterial communities, and its relative abundance accounted for 75.69%–80.23%. The combined process also enhanced carbohydrate metabolism and amino acid metabolism. Therefore, forced aeration coupled with semi-permeable membrane-covered represented a novel strategy for reducing global warming potential by regulating the structure and function of the bacterial communities during aerobic composting of dairy manure.

Sucrose-based biofloc system promotes the enrichment of specific gut bacterial taxa to enhance disease suppression in shrimp (Penaeus vannamei)

Sucrose-based biofloc system could facilitate the growth and fitness of shrimp (Penaeus vannamei) by regulating the gut bacterial community. However, little is known about the specific taxa enriched by sucrose-based biofloc system that could improve shrimp health. Here, we investigated the influences of sucrose-based biofloc system on the diversity, structure, and function of the shrimp gut bacterial community. Sucrose-based biofloc system enhanced the observed species and shannon index of the gut bacterial community, and altered the bacterial community compositions by aggrandizing the relative abundances of Amaricoccus, Demequina, and Microbacterium, and decreasing the abundances of potential pathogens belonging to Mycoplasmataceae. The relative abundances of three key operational taxonomic units (OTUs), Demequina OTU465, Microbacterium OTU778, and Amaricoccus OTU 3213 accounted for >50% contributions to shrimp growth and survival rate. Sucrose-based biofloc system positively improved the bacterial community functions involved in amino acid metabolism, metabolism of terpenoids and polyketides, and carbohydrate metabolism. These improved functions were also positively associated with these key OTUs, further implying that they might be key for shrimp health. Finally, the corresponding strains of these key OTUs were isolated to construct a synthetic community, which showed significantly promotive role in shrimp growth and resistance against pathogen challenge. These results not only help us understand the role of sucrose-based biofloc system in improving shrimp fitness better but also provide a reference for suppressing disease occurrence through the use of bacterial inocula.

Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables

Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal–Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.

Soil Bacterial Community Structure and Physicochemical Influencing Factors of Artificial Haloxylon ammodendron Forest in the Sand Blocking and Fixing Belt of Minqin, China

Microbial activity plays a crucial role in upholding the functional stability of vegetation–soil ecosystems. Nevertheless, there exists a paucity of studies concerning the impact of sand-fixing vegetation (Haloxylon ammodendron) on the structure and functional attributes of soil microbial communities. We employed Illumina high-throughput sequencing and PICRUSt2 functional prediction technology to investigate the characteristics of soil bacterial community structure, diversity, and metabolic functions in an artificial H. ammodendron forest, and RDA analysis and the Mantel test were used to reveal the main environmental factors affecting the structure and ecological functions of soil bacterial communities. The findings revealed a significant increase in the principal nutrient contents (organic matter, total nitrogen, total phosphorus) in the H. ammodendron forest soil compared to the mobile dune soil, while a reduction of 17.17% in the surface soil water content was observed. The H. ammodendron forest exhibited a significant enhancement in the diversity and richness index of soil bacteria. Specifically, Actinobacteria (24.94% ± 11.85%), Proteobacteria (29.99% ± 11.56%), and Chloroflexi (11.14% ± 4.55%) emerged as the dominant bacterial phyla, with Actinobacteria displaying significantly higher abundance compared to the mobile dune soil. PICRUSt2 analyses revealed that the predominant secondary metabolic functions of soil bacteria were carbohydrate metabolism, amino acid metabolism, and the metabolism of cofactors and vitamins. Additionally, the tertiary metabolic pathways exhibited greater activity in relation to enzyme function, nucleotide metabolism, energy metabolism, and antibiotics. The RDA results demonstrated that SOM, AK, and pH collectively accounted for 82.4% of the cumulative contribution, significantly influencing the bacterial community. Moreover, the Mantel test revealed that the metabolic function of soil bacteria primarily relied on five environmental factors, namely SOM, TN, AK, pH, and EC. This study significantly advances our understanding of the structural and functional changes in soil bacterial communities during the reclamation of sandy land through the establishment of artificial H. ammodendron forests.

The Assembly Process of Free-Living and Particle-Attached Bacterial Communities in Shrimp-Rearing Waters: The Overwhelming Influence of Nutrient Factors Relative to Microalgal Inoculation.

The ecological functions of bacterial communities vary between particle-attached (PA) lifestyles and free-living (FL) lifestyles, and separately exploring their community assembly helps to elucidate the microecological mechanisms of shrimp rearing. Microalgal inoculation and nutrient enrichment during shrimp rearing are two important driving factors that affect rearing-water bacterial communities, but their relative contributions to the bacterial community assembly have not been evaluated. Here, we inoculated two microalgae, Nannochloropsis oculata and Thalassiosira weissflogii, into shrimp-rearing waters to investigate the distinct effects of various environmental factors on PA and FL bacterial communities. Our study showed that the composition and representative bacteria of different microalgal treatments were significantly different between the PA and FL bacterial communities. Regression analyses and Mantel tests revealed that nutrients were vital factors that constrained the diversity, structure, and co-occurrence patterns of both the PA and FL bacterial communities. Partial least squares path modeling (PLS-PM) analysis indicated that microalgae could directly or indirectly affect the PA bacterial community through nutrient interactions. Moreover, a significant interaction was detected between PA and FL bacterial communities. Our study reveals the unequal effects of microalgae and nutrients on bacterial community assembly and helps explore microbial community assembly in shrimp-rearing ecosystems.

Effects of Vegetation Types and Seasonal Dynamics on the Diversity and Function of Soil Bacterial Communities in the Upper Reaches of the Heihe River

The process of interaction between the plant and soil microbial communities holds the key to understanding the biogeochemical cycle and preserving the stability of vegetation ecosystems. Owing to this significance, the primary goal of this research was to give a starting point and reference methods to restore local vegetation. The vegetation distribution in the mountainous area of the upper reaches of the Heihe River Basin had notable vertical zonality, which was characterized by five typical vegetation types, including cushion vegetation(CV), herbage meadow(HM), forest steppe(FS), mountainous steppe(MS), and desert grassland(DG). The organization and diversity of soil bacterial communities in various vegetation types were examined using high-throughput sequencing techniques in both the winter and summer seasons. Sampling sites were chosen in each of the five common vegetation types in turn. Additionally, based on the FAPROTAX database, the predicted functions of microbial communities were evaluated for different vegetation types and seasons. The redundancy analysis and structural equation model were also used to investigate the primary environmental elements and uncover the mechanisms affecting the soil bacterial populations. The findings revealed that:① the physical and chemical properties of soil differed significantly among vegetation types and seasons, and the property indices varied dissimilarly with depth. In particular, the soil water content(SWC) and nutrient content of total organic carbon(TOC) and total nitrogen(TN) were significantly higher in forest grassland(FS). ② The divergences of α-diversity indices among seasons(P<0.05) were greater than that of vegetation types(P>0.05). The Chao1 index measuring the abundance of the bacterial community was higher in winter. According to the Shannon index, the species of the bacterial community were dispersed in a "W" shape in the summer and a "hump" form in the winter with altitude. ③ The predominant phyla of the bacterial community, composed of Acidobacteria, Proteobacteria, and Actinobacteria, did not significantly differ from one another. However, the organization of the bacterial community presented a significant variation seasonally at the genus level. ④ The primary functions of the soil bacterial population, which largely consisted of chemoheterotrophy, nitrification, and aerobic ammonia oxidation, were not significantly different among vegetation types and seasons. ⑤ The key factors affecting soil bacterial communities at the genus level varied significantly among seasons, with soil temperature(ST), total organic carbon(TOC), and pH in winter and soil water content(SWC), carbon-nitrogen ratio(C/N), and pH in summer. ⑥ Synergized by interrelated environmental factors, soil physical and chemical features exerted a more direct impact on the diversity and functionality of bacterial communities compared with vegetation types, including significantly changing the abundance of Acidobacteria and Bacteroidetes, as well as the role of nitrification and ammonia oxidation. Hence, improving the carbon and nitrogen contents in soil nutrients would help to enhance the diversity and function of bacterial communities. The findings of this study provided a model for determining the mechanism of regional vegetation degradation and preserving the stability of alpine ecosystems in this area by revealing the seasonal distribution pattern of bacterial communities and the key biological processes beneath the typical vertical vegetation band in the upper reaches of the Heihe River.

Characterizing bacterial and fungal communities along the longitudinal axis of the intestine in cynomolgus monkeys

ABSTRACT The gut microbiota develops specialized local communities along the gastrointestinal (GI) tract of the host. Among these microbes, intestinal bacteria and fungi interact closely with the host and play vital roles in their health. However, the gut biogeography of bacteria and fungi has rarely been studied simultaneously, and their correlations have not been reported. In this study, we collected the intestinal luminal contents from different gastrointestinal regions (the ileum, caecum, and colon) of wild-type female cynomolgus monkeys and performed 16S and 18S rRNA gene sequencing to determine the gut biogeography of bacterial and fungal communities. The richness and diversity of bacteria and fungi increased gradually from the small to the large intestine. The bacterial and fungal composition of ileum differed significantly from that of the colon. Specifically, Bacteroidia and Spirochaetia were abundant in the caecum and colon, while Actinobacteria and Cyanobacteria were enriched in the ileum. As for fungal taxa, the genera Aspergillus , Wallemia , and Cryptococcus_f_Tremellaceae were enriched in the colon, while the genus Fusarium was abundant in the caecum. Consequently, the bacterial and fungal functions of the ileum differed from those of the caecum and colon. Notably, we characterized the correlations between intestinal bacteria and fungi at different gastrointestinal regions of cynomolgus monkeys using Spearman correlation analysis. In summary, our results contribute to a more comprehensive understanding of the composition and function of intestinal bacteria and fungi in non-human primates (NHPs) and reveal their correlations along the longitudinal axis of the intestine. IMPORTANCE Gut microbiota varies along the gastrointestinal (GI) tract and exerts profound influences on the host’s physiology, immunity, and nutrition. Given that gut microbes interact with the host closely and the gastrointestinal function differed from the small to the large intestine, it is essential to characterize the gut biogeography of the microbial community. Here, we focused on intestinal bacteria and fungi in cynomolgus monkeys and determined their spatial distribution along the GI tract by performing 16S and 18S rRNA gene sequencing. The composition and function of bacterial and fungal communities differed significantly at different biogeographic sites of the intestine, and the site-specific correlations between intestinal bacteria and fungi were revealed. Thus, our studies characterized the gut biogeography of bacteria and fungi in NHPs and revealed their site-specific correlations along the GI tract.